[2021-09-29 01:17:07,115] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2021-09-29 01:17:07,116] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2021-09-29 01:17:07,116] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2021-09-29 01:17:07,117] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml [2021-09-29 01:17:07,117] multiqc [DEBUG ] New config 'report_section_order': {'demux_report': {'after': 'run_stats'}} [2021-09-29 01:17:07,117] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKCW5DRXY/merged [2021-09-29 01:17:08,483] multiqc [WARNING] MultiQC Version v1.11 now available! [2021-09-29 01:17:08,483] multiqc [INFO ] This is MultiQC v1.9 [2021-09-29 01:17:08,483] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/hpcpipe/mqc_config.yaml /scratch/gencore/logs/html/HKCW5DRXY/merged [2021-09-29 01:17:08,483] multiqc [DEBUG ] Working dir : /scratch/gencore/logs/html/HKCW5DRXY/merged [2021-09-29 01:17:08,483] multiqc [INFO ] Template : default [2021-09-29 01:17:08,483] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2021-09-29 01:17:08,483] multiqc [INFO ] Searching : /scratch/gencore/logs/html/HKCW5DRXY/merged [2021-09-29 01:17:08,483] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, snpsplit, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, kaiju, kraken, malt, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, pycoqc, minionqc, multivcfanalyzer, clusterflow, bcl2fastq, interop, ivar, flash, seqyclean [2021-09-29 01:17:08,484] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-10373561/tmp2sx_fws3 [2021-09-29 01:17:08,586] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-29 01:17:08,588] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-29 01:17:08,588] multiqc [DEBUG ] File ignored by rockhopper because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-29 01:17:08,588] multiqc [DEBUG ] File ignored by rseqc/bam_stat because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-29 01:17:08,588] multiqc [DEBUG ] File ignored by rseqc/junction_annotation because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-29 01:17:08,588] multiqc [DEBUG ] File ignored by rseqc/read_distribution because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-29 01:17:08,588] multiqc [DEBUG ] File ignored by rseqc/infer_experiment because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-29 01:17:08,636] multiqc [DEBUG ] File ignored by stacks/sumstats because it exceeded search pattern filesize limit: undetermined_barcodes.txt [2021-09-29 01:17:10,669] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKCW5DRXY_n02_DJ62_2_fastqc.html [2021-09-29 01:17:10,671] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKCW5DRXY_n02_DJ62_2_fastqc.html [2021-09-29 01:17:10,728] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKCW5DRXY_n02_DJ63_2_fastqc.html [2021-09-29 01:17:10,729] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKCW5DRXY_n02_DJ63_2_fastqc.html [2021-09-29 01:17:10,768] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKCW5DRXY_n01_JK11_2_fastqc.html [2021-09-29 01:17:10,770] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKCW5DRXY_n01_JK11_2_fastqc.html [2021-09-29 01:17:10,809] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKCW5DRXY_n02_JK12_2_fastqc.html [2021-09-29 01:17:10,810] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKCW5DRXY_n02_JK12_2_fastqc.html [2021-09-29 01:17:10,860] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKCW5DRXY_n01_undetermined_fastqc.html [2021-09-29 01:17:10,862] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKCW5DRXY_n01_undetermined_fastqc.html [2021-09-29 01:17:10,900] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKCW5DRXY_n01_JK12_2_fastqc.html [2021-09-29 01:17:10,902] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKCW5DRXY_n01_JK12_2_fastqc.html [2021-09-29 01:17:10,954] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKCW5DRXY_n01_DJ62_2_fastqc.html [2021-09-29 01:17:10,956] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKCW5DRXY_n01_DJ62_2_fastqc.html [2021-09-29 01:17:11,015] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKCW5DRXY_n02_undetermined_fastqc.html [2021-09-29 01:17:11,017] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKCW5DRXY_n02_undetermined_fastqc.html [2021-09-29 01:17:11,068] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKCW5DRXY_n01_DJ63_2_fastqc.html [2021-09-29 01:17:11,069] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKCW5DRXY_n01_DJ63_2_fastqc.html [2021-09-29 01:17:11,107] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: HKCW5DRXY_n02_JK11_2_fastqc.html [2021-09-29 01:17:11,109] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: HKCW5DRXY_n02_JK11_2_fastqc.html [2021-09-29 01:17:11,424] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-29 01:17:11,425] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2021-09-29 01:17:11,434] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 5 samples (table) [2021-09-29 01:17:11,436] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2021-09-29 01:17:11,446] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2021-09-29 01:17:11,450] multiqc [DEBUG ] No samples found: conpair [2021-09-29 01:17:11,456] multiqc [DEBUG ] No samples found: peddy [2021-09-29 01:17:11,462] multiqc [DEBUG ] No samples found: somalier [2021-09-29 01:17:11,467] multiqc [DEBUG ] No samples found: methylQA [2021-09-29 01:17:11,478] multiqc [DEBUG ] No samples found: mosdepth [2021-09-29 01:17:11,483] multiqc [DEBUG ] No samples found: phantompeakqualtools [2021-09-29 01:17:11,486] multiqc [DEBUG ] No samples found: qualimap [2021-09-29 01:17:11,492] multiqc [DEBUG ] No samples found: preseq [2021-09-29 01:17:11,496] multiqc [DEBUG ] No samples found: quast [2021-09-29 01:17:11,500] multiqc [DEBUG ] No samples found: qorts [2021-09-29 01:17:11,504] multiqc [DEBUG ] No samples found: rna_seqc [2021-09-29 01:17:11,510] multiqc [DEBUG ] No samples found: rockhopper [2021-09-29 01:17:11,515] multiqc [DEBUG ] No samples found: rsem [2021-09-29 01:17:11,528] multiqc [DEBUG ] No samples found: rseqc [2021-09-29 01:17:11,532] multiqc [DEBUG ] No samples found: busco [2021-09-29 01:17:11,536] multiqc [DEBUG ] No samples found: goleft_indexcov [2021-09-29 01:17:11,542] multiqc [DEBUG ] No samples found: disambiguate [2021-09-29 01:17:11,546] multiqc [DEBUG ] No samples found: supernova [2021-09-29 01:17:11,562] multiqc [DEBUG ] No samples found: deeptools [2021-09-29 01:17:11,566] multiqc [DEBUG ] No samples found: sargasso [2021-09-29 01:17:11,574] multiqc [DEBUG ] No samples found: verifybamid [2021-09-29 01:17:11,578] multiqc [DEBUG ] No samples found: mirtrace [2021-09-29 01:17:11,583] multiqc [DEBUG ] No samples found: happy [2021-09-29 01:17:11,588] multiqc [DEBUG ] No samples found: mirtop [2021-09-29 01:17:11,597] multiqc [DEBUG ] No samples found: homer [2021-09-29 01:17:11,601] multiqc [DEBUG ] No samples found: macs2 [2021-09-29 01:17:11,606] multiqc [DEBUG ] No samples found: theta2 [2021-09-29 01:17:11,611] multiqc [DEBUG ] No samples found: snpeff [2021-09-29 01:17:11,618] multiqc [DEBUG ] No samples found: gatk [2021-09-29 01:17:11,624] multiqc [DEBUG ] No samples found: htseq [2021-09-29 01:17:11,629] multiqc [DEBUG ] No samples found: bcftools [2021-09-29 01:17:11,633] multiqc [DEBUG ] No samples found: featureCounts [2021-09-29 01:17:11,642] multiqc [DEBUG ] No samples found: fgbio [2021-09-29 01:17:11,659] multiqc [DEBUG ] No samples found: dragen [2021-09-29 01:17:11,665] multiqc [DEBUG ] No samples found: dedup [2021-09-29 01:17:11,670] multiqc [DEBUG ] No samples found: damageprofiler [2021-09-29 01:17:11,696] multiqc [DEBUG ] No samples found: biobambam2 [2021-09-29 01:17:11,702] multiqc [DEBUG ] No samples found: mtnucratio [2021-09-29 01:17:11,704] multiqc [DEBUG ] No samples found: picard [2021-09-29 01:17:11,708] multiqc [DEBUG ] No samples found: prokka [2021-09-29 01:17:11,712] multiqc [DEBUG ] No samples found: samblaster [2021-09-29 01:17:11,724] multiqc [DEBUG ] No samples found: samtools [2021-09-29 01:17:11,728] multiqc [DEBUG ] No samples found: sexdeterrmine [2021-09-29 01:17:11,733] multiqc [DEBUG ] No samples found: bamtools [2021-09-29 01:17:11,738] multiqc [DEBUG ] No samples found: jellyfish [2021-09-29 01:17:11,744] multiqc [DEBUG ] No samples found: vcftools [2021-09-29 01:17:11,750] multiqc [DEBUG ] No samples found: longranger [2021-09-29 01:17:11,755] multiqc [DEBUG ] No samples found: stacks [2021-09-29 01:17:11,761] multiqc [DEBUG ] No samples found: varscan2 [2021-09-29 01:17:11,780] multiqc [DEBUG ] No samples found: bbmap [2021-09-29 01:17:11,784] multiqc [DEBUG ] No samples found: bismark [2021-09-29 01:17:11,791] multiqc [DEBUG ] No samples found: biscuit [2021-09-29 01:17:11,796] multiqc [DEBUG ] No samples found: hicexplorer [2021-09-29 01:17:11,800] multiqc [DEBUG ] No samples found: hicup [2021-09-29 01:17:11,806] multiqc [DEBUG ] No samples found: hicpro [2021-09-29 01:17:11,811] multiqc [DEBUG ] No samples found: salmon [2021-09-29 01:17:11,815] multiqc [DEBUG ] No samples found: kallisto [2021-09-29 01:17:11,823] multiqc [DEBUG ] No samples found: slamdunk [2021-09-29 01:17:11,827] multiqc [DEBUG ] No samples found: star [2021-09-29 01:17:11,831] multiqc [DEBUG ] No samples found: hisat2 [2021-09-29 01:17:11,836] multiqc [DEBUG ] No samples found: tophat [2021-09-29 01:17:11,842] multiqc [DEBUG ] No samples found: bowtie2 [2021-09-29 01:17:11,848] multiqc [DEBUG ] No samples found: bowtie1 [2021-09-29 01:17:11,852] multiqc [DEBUG ] No samples found: snpsplit [2021-09-29 01:17:11,856] multiqc [DEBUG ] No samples found: kat [2021-09-29 01:17:11,860] multiqc [DEBUG ] No samples found: leehom [2021-09-29 01:17:11,865] multiqc [DEBUG ] No samples found: adapterRemoval [2021-09-29 01:17:11,869] multiqc [DEBUG ] No samples found: clipandmerge [2021-09-29 01:17:11,873] multiqc [DEBUG ] No samples found: cutadapt [2021-09-29 01:17:11,879] multiqc [DEBUG ] No samples found: flexbar [2021-09-29 01:17:11,884] multiqc [DEBUG ] No samples found: kaiju [2021-09-29 01:17:11,890] multiqc [DEBUG ] No samples found: kraken [2021-09-29 01:17:11,894] multiqc [DEBUG ] No samples found: malt [2021-09-29 01:17:11,899] multiqc [DEBUG ] No samples found: trimmomatic [2021-09-29 01:17:11,903] multiqc [DEBUG ] No samples found: sickle [2021-09-29 01:17:11,907] multiqc [DEBUG ] No samples found: skewer [2021-09-29 01:17:11,913] multiqc [DEBUG ] No samples found: sortmerna [2021-09-29 01:17:11,917] multiqc [DEBUG ] No samples found: biobloomtools [2021-09-29 01:17:11,921] multiqc [DEBUG ] No samples found: fastq_screen [2021-09-29 01:17:11,926] multiqc [DEBUG ] No samples found: afterqc [2021-09-29 01:17:11,932] multiqc [DEBUG ] No samples found: fastp [2021-09-29 01:17:12,416] multiqc.modules.fastqc.fastqc [INFO ] Found 10 reports [2021-09-29 01:17:12,563] multiqc [DEBUG ] No samples found: pycoqc [2021-09-29 01:17:12,594] multiqc [DEBUG ] No samples found: minionqc [2021-09-29 01:17:12,598] multiqc [DEBUG ] No samples found: multivcfanalyzer [2021-09-29 01:17:12,603] multiqc [DEBUG ] No samples found: clusterflow [2021-09-29 01:17:12,609] multiqc [DEBUG ] No samples found: bcl2fastq [2021-09-29 01:17:12,613] multiqc [DEBUG ] No samples found: interop [2021-09-29 01:17:12,619] multiqc [DEBUG ] No samples found: ivar [2021-09-29 01:17:12,625] multiqc [DEBUG ] No samples found: flash [2021-09-29 01:17:12,632] multiqc [DEBUG ] No samples found: seqyclean [2021-09-29 01:17:12,633] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2021-09-29 01:17:12,633] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2021-09-29 01:17:12,633] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2021-09-29 01:17:12,633] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2021-09-29 01:17:12,645] multiqc [INFO ] Compressing plot data [2021-09-29 01:17:12,825] multiqc [INFO ] Report : multiqc_report.html [2021-09-29 01:17:12,825] multiqc [INFO ] Data : multiqc_data [2021-09-29 01:17:12,825] multiqc [DEBUG ] Moving data file from '/state/partition1/job-10373561/tmp2sx_fws3/multiqc_data' to '/scratch/gencore/logs/html/HKCW5DRXY/merged/multiqc_data' [2021-09-29 01:17:12,938] multiqc [INFO ] MultiQC complete